The most common quantitative measurements made with optical coherence tomography (OCT) are thickness measurements. Examples include total retinal thickness in the macular area, retinal nerve fiber layer thickness (RNFL) in the peripapillary area, and other layer thicknesses such as ganglion cell complex thicknesses. For instance, the standard measurement used to assess edema or atrophy of the retina is a measurement of the thickness of the entire retina from the Internal Limiting Membrane (ILM) to the Retinal Pigment Epithelium (RPE). However, the visual acuity of a patient before or after treatment may bear little relation to thickness measurements. A more relevant assessment to some diseases, especially diseases known to affect the photoreceptor layer, may be made by analyzing images so as to assess the status of the photoreceptors, but thickness measurements may not be the most appropriate way of assessing the health of the photoreceptors. For example, the true thickness of a particular retinal layer may not vary smoothly with increasing pathology, but rather may exhibit more of a two-state behavior: either it appears healthy at a particular location or it does not, and the sign of the extent of pathology is the area of unhealthy tissue. Furthermore, the first signs of disease in a particular layer may be observed as disruptions that maintain most of the average thickness of the layer. These disruptions may be seen as alterations or variations in thickness, reflectivity, or other properties over an area of observation. An algorithm that attempts to give a consistent contour over disrupted areas may actually smooth out some local variations in tissue integrity and obscure signs of pathology.